Ontology-based representations are gaining momentum among other alternatives for implementing the knowledge model of high-level fusion applications. In this paper, we provide an introduction to the theoretical foundations of ontology-based knowledge representation and reasoning, with a particular focus on the issues that appear in maritime security, where heterogeneous regulations, information sources, users, and systems are involved. We also present some current approaches and existing technologies for high-level fusion, based on ontological representations. Unfortunately, current tools for the practical implementation of ontology-based systems are not fully standardized or even prepared to work together in medium-scale systems. Accordingly, we discuss different alternatives to face problems such as spatial and temporal knowledge representation or uncertainty management. To illustrate the conclusions drawn from this research, an ontology-based semantic tracking system is briefly presented. Results and latent capabilities of this framework are shown at the end of the paper, where we also envision future opportunities for this kind of application.